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Top Forums Shell Programming and Scripting Errors trying to use all files of a type Post 302955242 by Corona688 on Tuesday 15th of September 2015 05:04:58 PM
Old 09-15-2015
You are just removing the '.bam', you are not removing the long pathname.

Try FILE=$(basename "$FILE") to remove the path.
 

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RM(1)								   User Commands							     RM(1)

NAME
rm - remove files or directories SYNOPSIS
rm [OPTION]... [FILE]... DESCRIPTION
This manual page documents the GNU version of rm. rm removes each specified file. By default, it does not remove directories. If the -I or --interactive=once option is given, and there are more than three files or the -r, -R, or --recursive are given, then rm prompts the user for whether to proceed with the entire operation. If the response is not affirmative, the entire command is aborted. Otherwise, if a file is unwritable, standard input is a terminal, and the -f or --force option is not given, or the -i or --interac- tive=always option is given, rm prompts the user for whether to remove the file. If the response is not affirmative, the file is skipped. OPTIONS
Remove (unlink) the FILE(s). -f, --force ignore nonexistent files and arguments, never prompt -i prompt before every removal -I prompt once before removing more than three files, or when removing recursively; less intrusive than -i, while still giving protec- tion against most mistakes --interactive[=WHEN] prompt according to WHEN: never, once (-I), or always (-i); without WHEN, prompt always --one-file-system when removing a hierarchy recursively, skip any directory that is on a file system different from that of the corresponding command line argument --no-preserve-root do not treat '/' specially --preserve-root do not remove '/' (default) -r, -R, --recursive remove directories and their contents recursively -d, --dir remove empty directories -v, --verbose explain what is being done --help display this help and exit --version output version information and exit By default, rm does not remove directories. Use the --recursive (-r or -R) option to remove each listed directory, too, along with all of its contents. To remove a file whose name starts with a '-', for example '-foo', use one of these commands: rm -- -foo rm ./-foo Note that if you use rm to remove a file, it might be possible to recover some of its contents, given sufficient expertise and/or time. For greater assurance that the contents are truly unrecoverable, consider using shred. AUTHOR
Written by Paul Rubin, David MacKenzie, Richard M. Stallman, and Jim Meyering. REPORTING BUGS
GNU coreutils online help: <http://www.gnu.org/software/coreutils/> Report rm translation bugs to <http://translationproject.org/team/> COPYRIGHT
Copyright (C) 2017 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. SEE ALSO
unlink(1), unlink(2), chattr(1), shred(1) Full documentation at: <http://www.gnu.org/software/coreutils/rm> or available locally via: info '(coreutils) rm invocation' GNU coreutils 8.28 January 2018 RM(1)
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